Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus

A lattice model with side chains was used to investigate protein folding wi th computer simulations. In this model, we rigorously demonstrate the exist ence of a specific folding nucleus. This nucleus contains specific interact ions not present in the native state that, when weakened, slow folding but do not change protein stability. Such a decoupling of folding kinetics from thermodynamics has been observed experimentally for real proteins. From ou r results, we conclude that specific non-native interactions in the transit ion state would give rise to phi-values that are negative or larger than un ity. Furthermore, we demonstrate that residue lie 34 in src SH3, which has been shown to be kinetically, but not thermodynamically, important, is univ ersally conserved in proteins with the SH3 fold. This is a clear example of evolution optimizing the folding rate of a protein independent of its stab ility and function.